! The ARCS/ARKS projects have now been consolidated. The ARKS functionality is available from:

Important Note

ARKS has been integrated into as of version 1.1.0

To run ARCS in ARKS mode:

arcs --arks [options] <linked reads fastq>

The full ARKS pipeline can be run with the supplied Makefile:

Examples/arcs-make arks draft=myassembly reads=myreads

Future code maintenance for ARKS will be done in the ARCS repository ONLY.

ARKS

Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. This project is a new kmer-based (alignment free) implementation of ARCS. It provides improved runtime performance over the original ARCS implementation by removing the requirement to perform alignments with bwa mem.

Dependencies

Boost (tested on 1.61)
GCC (tested on 4.4.7)
Autotools (if cloning directly from repository)
LINKS (tested on 1.8)

Installation:

Install ARKS using Brew

brew install brewsci/bio/arks

Install ARKS from the source code

If cloning directly from the repository run:

./autogen.sh

To compile ARKS run:

./configure && make

To install ARKS in a specified directory:

./configure --prefix=/ARKS/PATH && make install

If your boost library headers are not in your PATH you can specify their location:

./configure –-with-boost=/boost/path --prefix=/ARKS/PATH && make install

ARKS+LINKS Pipeline

ARKS requires three input files:

Draft assembly fasta file
Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header; Run Long Ranger basic on raw chromium reads to produce this interleaved file)
CSV file listing barcode multiplicities (Generate with command: bin/calcBarcodeMultiplicities.pl reads.fof > read_multiplicities.csv, where reads.fof is file with name of linked read file)

The Makefile located here: Examples/arks-make will run the full ARKS pipeline, including generating the barcode multiplicity file above, and the 3 steps below. It will also optionally run the misassembly corrector Tigmint prior to scaffolding with ARKS.

There are three steps to the pipeline:

Run ARKS to generate a Graphviz Dot file (.gv). Nodes in the graph are the sequences to scaffold, and edges show that there is evidence to suggest nodes are linked based on the data obtained from the GemCode/Chromium reads.
Run the python script Examples/makeTSVfile.py to generate a file named XXX.tigpair_checkpoint file from the ARKS graph file. The XXX.tigpair_checkpoint file will be provided to LINKS in step 3.
Run LINKS with the XXX.tigpair_checkpoint file as input. To do this, the base name (-b) must be set to the same name as XXX.

An example bash script on how to run the ARKS+LINKS pipeline using the ARKS Makefile can be found at: Examples/pipeline_example.sh

you can test your installation by following instructions at: Examples/arks_test-demo/README.txt and compare your output to the files provided at: Examples/arks_test-demo/output/

Citing ARKS

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.
Coombe L, Zhang J, Vandervalk BP, Chu J, Jackman SD, Birol I, Warren RL.
BMC Bioinformatics. 2018 Jun 20;19(1):234. doi: 10.1186/s12859-018-2243-x.

Citing ARCS

ARCS: scaffolding genome drafts with linked reads.
Yeo S, Coombe L, Warren RL, Chu J, Birol I.
Bioinformatics. 2018 Mar 1;34(5):725-731. doi: 10.1093/bioinformatics/btx675.

NOTE: The supplementary data and scripts have been moved to http://www.bcgsc.ca/downloads/supplementary/ARCS/

Citing LINKS :

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads.
Warren RL, Yang C, Vandervalk BP, Behsaz B, Lagman A, Jones SJ, Birol I.
Gigascience. 2015 Aug 4;4:35. doi: 10.1186/s13742-015-0076-3. eCollection 2015.

License

ARKS is released under the GNU General Public License v3

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, version 3.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

For commercial licensing options, please contact Patrick Rebstein prebstein@bccancer.bc.ca

bcgsc/arks